Search results for the GEO ID: GSE23293  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM571720 | GPL570 |
|
healthy CD4 cells - after stimulation - proband4
|
CD4 cells - after stimulation - proband4 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 41
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571720
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571720/suppl/GSM571720_P4_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571721 | GPL570 |
|
FL CD4 cells - after stimulation - proband5
|
CD4 cells - after stimulation - proband5 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 65
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571721
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571721/suppl/GSM571721_P5_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571722 | GPL570 |
|
CLL CD4 cells - after stimulation - proband7
|
CD4 cells - after stimulation - proband7 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 53
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571722
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571722/suppl/GSM571722_P7_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571723 | GPL570 |
|
MALT CD4 cells - after stimulation - proband8
|
CD4 cells - after stimulation - proband8 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MALT
age in years: 65
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571723
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571723/suppl/GSM571723_P8_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571724 | GPL570 |
|
FL CD4 cells - after stimulation - proband9
|
CD4 cells - after stimulation - proband9 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 51
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571724
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571724/suppl/GSM571724_P9_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571725 | GPL570 |
|
FL CD4 cells - after stimulation - proband10
|
CD4 cells - after stimulation - proband10 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 37
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571725
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571725/suppl/GSM571725_P10_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571726 | GPL570 |
|
CLL CD4 cells - after stimulation - proband11
|
CD4 cells - after stimulation - proband11 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 72
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571726
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571726/suppl/GSM571726_P11_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571727 | GPL570 |
|
MALT CD4 cells - after stimulation - proband12
|
CD4 cells - after stimulation - proband12 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MALT
age in years: 77
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571727
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571727/suppl/GSM571727_P12_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571728 | GPL570 |
|
FL CD4 cells - after stimulation - proband14
|
CD4 cells - after stimulation - proband14 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 60
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571728
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571728/suppl/GSM571728_P14_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571729 | GPL570 |
|
FL CD4 cells - after stimulation - proband15
|
CD4 cells - after stimulation - proband15 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 66
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571729
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571729/suppl/GSM571729_P15_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571730 | GPL570 |
|
CLL CD4 cells - after stimulation - proband16
|
CD4 cells - after stimulation - proband16 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 54
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571730
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571730/suppl/GSM571730_P16_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571731 | GPL570 |
|
CLL CD4 cells - after stimulation - proband17
|
CD4 cells - after stimulation - proband17 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 42
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571731
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571731/suppl/GSM571731_P17_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571732 | GPL570 |
|
CLL CD4 cells - after stimulation - proband18
|
CD4 cells - after stimulation - proband18 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 60
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571732
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571732/suppl/GSM571732_P18_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571733 | GPL570 |
|
MGUS CD4 cells - after stimulation - proband19
|
CD4 cells - after stimulation - proband19 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MGUS
age in years: 55
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571733
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571733/suppl/GSM571733_P19_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571734 | GPL570 |
|
MGUS CD4 cells - after stimulation - proband20
|
CD4 cells - after stimulation - proband20 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MGUS
age in years: 43
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571734
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571734/suppl/GSM571734_P20_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571735 | GPL570 |
|
MALT CD4 cells - after stimulation - proband21
|
CD4 cells - after stimulation - proband21 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MALT
age in years: 49
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571735
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571735/suppl/GSM571735_P21_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571736 | GPL570 |
|
FL CD4 cells - after stimulation - proband22
|
CD4 cells - after stimulation - proband22 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 64
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571736
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571736/suppl/GSM571736_P22_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571737 | GPL570 |
|
MGUS CD4 cells - after stimulation - proband23
|
CD4 cells - after stimulation - proband23 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MGUS
age in years: 50
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571737
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571737/suppl/GSM571737_P23_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571738 | GPL570 |
|
CLL CD4 cells - after stimulation - proband24
|
CD4 cells - after stimulation - proband24 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 74
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571738
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571738/suppl/GSM571738_P24_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571739 | GPL570 |
|
CLL CD4 cells - after stimulation - proband25
|
CD4 cells - after stimulation - proband25 - rep1
|
cell type: peripheral blood CD4 cells
disease state: CLL
age in years: 66
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571739
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571739/suppl/GSM571739_P25_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571740 | GPL570 |
|
MGUS CD4 cells - after stimulation - proband26
|
CD4 cells - after stimulation - proband26 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MGUS
age in years: 66
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571740
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571740/suppl/GSM571740_P26_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571741 | GPL570 |
|
healthy CD4 cells - after stimulation - proband27
|
CD4 cells - after stimulation - proband27 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 51
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571741
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571741/suppl/GSM571741_P27_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571742 | GPL570 |
|
healthy CD4 cells - after stimulation - proband28
|
CD4 cells - after stimulation - proband28 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 43
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571742
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571742/suppl/GSM571742_P28_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571743 | GPL570 |
|
healthy CD4 cells - after stimulation - proband29
|
CD4 cells - after stimulation - proband29 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 60
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571743
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571743/suppl/GSM571743_P29_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571744 | GPL570 |
|
MALT CD4 cells - after stimulation - proband30
|
CD4 cells - after stimulation - proband30 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MALT
age in years: 56
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571744
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571744/suppl/GSM571744_P30_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571745 | GPL570 |
|
healthy CD4 cells - after stimulation - proband31
|
CD4 cells - after stimulation - proband31 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 65
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571745
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571745/suppl/GSM571745_P31_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571746 | GPL570 |
|
healthy CD4 cells - after stimulation - proband32
|
CD4 cells - after stimulation - proband32 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 63
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571746
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571746/suppl/GSM571746_P32_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571747 | GPL570 |
|
healthy CD4 cells - after stimulation - proband33
|
CD4 cells - after stimulation - proband33 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 65
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571747
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571747/suppl/GSM571747_P33_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571748 | GPL570 |
|
healthy CD4 cells - after stimulation - proband34
|
CD4 cells - after stimulation - proband34 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 51
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571748
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571748/suppl/GSM571748_P34_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571749 | GPL570 |
|
healthy CD4 cells - after stimulation - proband35
|
CD4 cells - after stimulation - proband35 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 64
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571749
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571749/suppl/GSM571749_P35_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571750 | GPL570 |
|
healthy CD4 cells - after stimulation - proband36
|
CD4 cells - after stimulation - proband36 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 76
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571750
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571750/suppl/GSM571750_P36_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571751 | GPL570 |
|
healthy CD4 cells - after stimulation - proband37
|
CD4 cells - after stimulation - proband37 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 64
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571751
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571751/suppl/GSM571751_P37_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571752 | GPL570 |
|
healthy CD4 cells - after stimulation - proband38
|
CD4 cells - after stimulation - proband38 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 70
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 1
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571752
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571752/suppl/GSM571752_P38_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571753 | GPL570 |
|
healthy CD4 cells - after stimulation - proband39
|
CD4 cells - after stimulation - proband39 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 62
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571753
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571753/suppl/GSM571753_P39_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571754 | GPL570 |
|
healthy CD4 cells - after stimulation - proband40
|
CD4 cells - after stimulation - proband40 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 64
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571754
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571754/suppl/GSM571754_P40_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571755 | GPL570 |
|
MGUS CD4 cells - after stimulation - proband41
|
CD4 cells - after stimulation - proband41 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MGUS
age in years: 59
used in fl/emzl vs healthy comparison (1-yes): 0
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571755
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571755/suppl/GSM571755_P41_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571756 | GPL570 |
|
FL CD4 cells - after stimulation - proband42
|
CD4 cells - after stimulation - proband42 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 42
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571756
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571756/suppl/GSM571756_P42_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571757 | GPL570 |
|
MALT CD4 cells - after stimulation - proband43
|
CD4 cells - after stimulation - proband43 - rep1
|
cell type: peripheral blood CD4 cells
disease state: MALT
age in years: 35
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571757
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571757/suppl/GSM571757_P43_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571758 | GPL570 |
|
healthy CD4 cells - after stimulation - proband44
|
CD4 cells - after stimulation - proband44 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 49
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 1
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571758
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571758/suppl/GSM571758_P44_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571759 | GPL570 |
|
FL CD4 cells - after stimulation - proband45
|
CD4 cells - after stimulation - proband45 - rep1
|
cell type: peripheral blood CD4 cells
disease state: FL
age in years: 68
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571759
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571759/suppl/GSM571759_P45_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
|
GSM571760 | GPL570 |
|
healthy CD4 cells - after stimulation - proband46
|
CD4 cells - after stimulation - proband46 - rep1
|
cell type: peripheral blood CD4 cells
disease state: healthy
age in years: 36
used in fl/emzl vs healthy comparison (1-yes): 1
used in cll vs healthy comparison (1-yes): 0
used in mgus vs healthy comparison (1-yes): 0
|
peripheral blood CD4 cells, purified (>95% purity), after 40h of in vitro stimulation (10e5 cells/well, 100μl/well) on CD3-coated plates (BD Biosciences Biocoat) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions
Gene expression data from peripheral blood CD4 cells after in vitro stimulation with anti-CD3 and anti-CD28 for 40 h
|
| Sample_geo_accession | GSM571760
| | Sample_status | Public on Mar 01 2011
| | Sample_submission_date | Jul 28 2010
| | Sample_last_update_date | Mar 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling and activation phenotyping, 10e5 purified CD4+ T cells were stimulated (10e6 cells/ml) on CD3-coated plates (BD Biosciences) with 3 µg/ml anti-CD28 (BD Biosciences) in AIM-V medium (Invitrogen) under serum-free conditions. After 40 h, cells were harvested and preserved in RNAlater (Ambion).
| | Sample_growth_protocol_ch1 | CD4+ T cells were obtained from heparinized blood by Ficoll-Hypaque density gradient centrifugation and enriched to >95% purity (CD4+ T-cell isolation kit; Miltenyi Biotech) as verified by flow cytometry. In the case of CLL samples, B cells were depleted with microbead-conjugated CD19 antibodies (Miltenyi) prior to T cell purification.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cryopreserved cell lysates (RNeasy Mini kit, QIAGEN), precipitated with ethanol, and reconstituted at 0.5 µg/µl. RNA quality was confirmed by a median RNA integrity number of 10 (range: 9.3-10) (Agilent 2100 Bioanalyzer; Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 μg total RNA with the Affymetrix “One-Cycle kit” (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)
| | Sample_data_processing | Microarray data were analyzed with Expressionist v5.3.3 software (Genedata). Gene expression values for subsequent analyses were calculated from raw data (.CEL files) with GC-RMA condensation after quantile normalization. Groups of differentially regulated genes cells were determined with an unpaired t-test including estimation of false-positive results by Benjamini-Hochberg Q values. The samples used in each group of patients and control donors are denoted above in the columns H-I (column title: characteristics: used in xx vs healthy comparison). The gene expression profiles corresponding to external, non-expression data, like the production of IFNγ or IL-4 in FL/eMZL CD4 cells, were determined through a “profile distance search” as correlations of ranks. The statistical significance of overrepresentation of members of specific pathways among various groups of deregulated genes was tested with Fisher’s exact test after import of the KEGG pathway annotations included in the current Bioconductor package v2.5 (annotation package hgu133plus2.db v2.3.5) based on KEGG release 52 (September 2009), which includes 358 human pathways (www.bioconductor.org).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Petros,,Christopoulos
| | Sample_contact_department | Medizin I.
| | Sample_contact_institute | Uniklinik Freiburg
| | Sample_contact_address | Hugstetter Str. 55
| | Sample_contact_city | Freiburg
| | Sample_contact_zip/postal_code | 79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM571nnn/GSM571760/suppl/GSM571760_P46_stim_1.CEL.gz
| | Sample_series_id | GSE23293
| | Sample_data_row_count | 54675
| | |
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